Article
Genetics & Heredity
Kiely N. James, Shimul Chowdhury, Yan Ding, Sergey Batalov, Kelly Watkins, Yong Hyun Kwon, Lucitia Van Der Kraan, Katarzyna Ellsworth, Stephen F. Kingsmore, Lucia Guidugli
Summary: This study used genome sequencing to detect a wide range of copy-number variants (CNVs) and other non-single nucleotide variant/indel variant types. These genetic alterations accounted for 15.8% of reported variants, with deletions being the most common type. The study also found that additional genetic tests were ordered in some cases, but failed to report the variants detected by genome sequencing.
GENETICS IN MEDICINE
(2024)
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Cell Biology
Hao-Tian Wang, Long Zhao, Li-Qin Yang, Ming-Xia Ge, Xing-Li Yang, Zong-Liang Gao, Yu-Peng Cun, Fu-Hui Xiao, Qing-Peng Kong
Summary: By analyzing the whole genome somatic mutation profiles in 73 centenarians and 51 younger controls in China, researchers found that centenarian genomes have a skewed distribution of somatic mutations, with many genomic regions being conserved but having a high function potential. Additionally, long-lived individuals were observed to have more efficient DNA repair ability, supporting the idea that key genomic regions play a crucial role in human survival during aging and are essential for longevity.
Article
Oncology
Dane Cheasley, Abhimanyu Nigam, Magnus Zethoven, Sally Hunter, Dariush Etemadmoghadam, Timothy Semple, Prue Allan, Mark S. Carey, Marta L. Fernandez, Amy Dawson, Martin Kobel, David G. Huntsman, Cecile Le Page, Anne-Marie Mes-Masson, Diane Provencher, Neville Hacker, Yunkai Gao, David Bowtell, Anna deFazio, Kylie L. Gorringe, Ian G. Campbell
Summary: Low-grade serous ovarian carcinoma (LGSOC) is linked with poor response to chemotherapy, emphasizing the importance of genomic analysis to identify new therapeutic targets. A comprehensive study of LGSOC patients revealed potential driver aberrations and protein expressions that could impact disease outcomes and treatment responses.
(c) 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
JOURNAL OF PATHOLOGY
(2021)
Article
Veterinary Sciences
Akansha Singh, Amit Kumar, Cedric Gondro, A. K. Pandey, Triveni Dutt, B. P. Mishra
Summary: In this study, GWAS was conducted to identify SNPs associated with milk protein and minerals in crossbred cows. Several significant SNPs were found, and candidate genes and related biological processes were identified.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Genetics & Heredity
Zhipeng Wang, Yuanyuan Guo, Shengwei Liu, Qingli Meng
Summary: Copy number variations (CNVs) are important structural variations that can cause significant phenotypic diversity. Identification of CNVs from different genetic backgrounds can achieve reliable CNVs mapping. Investigations on the characteristics of overlapping between CNV regions (CNVRs) and protein-coding genes (CNV genes) or miRNAs (CNV-miRNAs) can reveal the potential mechanisms of their regulation.
FRONTIERS IN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie M. Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Karim Karimi, Guoyu Hu, Shafagh Valipour, Younes Miar
Summary: This study presents the first genome-wide CNV analysis of American mink, using whole-genome sequence data from 100 individuals. The results suggest potential links between CNVs and mink behavior, fur quality, and immune response.
Article
Agriculture, Dairy & Animal Science
P. A. S. Fonseca, F. S. Schenkel, A. Canovas
Summary: This study investigated the genetic basis of stillbirth in dairy cattle and identified 31 potential functional candidate genes associated with reproductive performance.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Genetics & Heredity
Jill Rafalko, Erica Soster, Samantha Caldwell, Eyad Almasri, Thomas Westover, Vivian Weinblatt, Philip Cacheris
Summary: This study found that genome-wide cfDNA screening can detect chromosomal abnormalities beyond traditional screening, with an overall PPV of >70% for cases with subchromosomal CNVs. Isolated CNVs had a lower PPV of 61.0% compared to complex CNVs at 93.9%. Detected abnormalities included isolated deletions/duplications and unbalanced structural rearrangements.
GENETICS IN MEDICINE
(2021)
Article
Genetics & Heredity
Yen On Chan, Jana Biova, Anser Mahmood, Nicholas Dietz, Kristin Bilyeu, Maria Skrabisova, Trupti Joshi
Summary: The rapid growth of sequencing technology has made whole genome re-sequencing (WGRS) data widely available, providing insights into genomic variations and their impact on phenotypic differences in plants. The GenVarX toolset, backed by various genomic and phenotypic data, allows researchers to analyze and visualize these variations, facilitating plant research. It supports easy-to-use interfaces, efficient data processing scripts, and interactive visualizations.
FRONTIERS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
Behjat Ul Mudassir, Mashael Alhumaidi Alotaibi, Nadeem Kizilbash, Daliyah Alruwaili, Anwar Alruwaili, Modhi Alenezi, Zehra Agha
Summary: This study identifies novel copy number variations (CNVs) in Pakistani families with neurodevelopmental disorders, which are associated with disease onset and progression. The discovery of altered gene dosage has potential implications for diagnosis, disease management, and genetic counseling. These findings contribute to the understanding of genotype-phenotype expression and pave the way for future therapeutics and precision medicine research in Pakistan.
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Md. Panir Choudhury, Zihao Wang, Min Zhu, Shaohua Teng, Jing Yan, Shuwei Cao, Guoqiang Yi, Yuwen Liu, Yuying Liao, Zhonglin Tang
Summary: This study conducted a comprehensive analysis of copy number variations (CNVs) in different horse breeds, and identified genomic regions associated with miniature features. Functional annotation revealed the biological functions and adaptations related to these CNVs.
Article
Medicine, General & Internal
Maren Holand, Kaja C. G. Berg, Ina A. Eilertsen, Bodil Bjerkehagen, Matthias Kolberg, Kjetil Boye, Ole Christian Lingjaerde, Tormod K. Guren, Nils Mandahl, Eva van den Berg, Emanuela Palmerini, Sigbjorn Smeland, Piero Picci, Fredrik Mertens, Anita Sveen, Ragnhild A. Lothe
Summary: MPNSTs were classified into two transcriptomic subtypes: immune active type with sustained immune signals and favorable prognosis, and immune deficient type with aggressive disease course, PRC2 loss, and expression of potential therapeutic targets. Copy number-based proliferative transcriptomic signatures were associated with patient prognosis.
Article
Biology
Tejashree H. Modak, Robert Literman, Jonathan B. Puritz, Kevin M. Johnson, Erin M. Roberts, Dina Proestou, Ximing Guo, Marta Gomez-Chiarri, Rachel S. Schwartz
Summary: Genomic structural variations are widely observed in the eastern oyster, showing high interindividual variability and potential impacts on gene function; these variations may play a significant role in genetic diversity and evolutionary success.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Oncology
Ana Casado-Garcia, Marta Isidro-Hernandez, Ninad Oak, Andrea Mayado, Christine Mann-Ran, Javier Raboso-Gallego, Silvia Aleman-Arteaga, Alexandra Buhles, Dario Sterker, Elena G. Sanchez, Jorge Martinez-Cano, Oscar Blanco, Alberto Orfao, Diego Alonso-Lopez, Javier De Las Rivas, Susana Riesco, Pablo Prieto-Matos, Africa Gonzalez-Murillo, Francisco Javier Garcia Criado, Maria Begona Garcia Cenador, Thomas Radimerski, Manuel Ramirez-Orellana, Cesar Cobaleda, Jun J. Yang, Carolina Vicente-Duenas, Andreas Weiss, Kim E. Nichols, Isidro Sanchez-Garcia
Summary: This study demonstrates that early-life administration of the JAK1/2 inhibitor ruxolitinib significantly reduces the risk of B-ALL in mice. This finding presents a potential strategy for preventing the development of B-ALL.
Article
Multidisciplinary Sciences
Jasper Janssens, Sara Aibar, Ibrahim Ihsan Taskiran, Joy N. Ismail, Alicia Estacio Gomez, Gabriel Aughey, Katina Spanier, Florian De Rop, Carmen Bravo Gonzalez-Blas, Marc Dionne, Krista Grimes, Xiao Jiang Quan, Dafni Papasokrati, Gert Hulselmans, Samira Makhzami, Maxime De Waegeneer, Valerie Christiaens, Tony Southall, Stein Aerts
Summary: The study reveals the diversity of neuronal and glial cell types in the Drosophila brain and identifies gene regulatory networks (GRNs) controlling their identities. By analyzing chromatin accessibility and transcriptome data, the researchers identified thousands of regulatory regions and created enhancer GRNs for different cell types.
Article
Immunology
Pablo Juanes-Velasco, Alicia Landeira-Vinuela, Marina L. Garcia-Vaquero, Quentin Lecrevisse, Raquel Herrero, Antonio Ferruelo, Rafael Gongora, Fernando Corrales, Javier De Las Rivas, Jose A. Lorente, Angela-Patricia Hernandez, Manuel Fuentes
Summary: This study analyzed the immune profile of severe ARDS in COVID-19 patients using functional proteomics approaches. It found that the autoimmune profiles were correlated with disease severity and clinical progression, providing new perspectives for therapeutic development and biomarker identification in COVID-19 patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Santiago Bueno-Fortes, Julienne K. Muenzner, Alberto Berral-Gonzalez, Chuanpit Hampel, Pablo Lindner, Alexandra Berninger, Kerstin Huebner, Philipp Kunze, Tobias Baeuerle, Katharina Erlenbach-Wuensch, Jose Manuel Sanchez-Santos, Arndt Hartmann, Javier de las Rivas, Regine Schneider-Stock
Summary: In this study, a gene signature associated with the loss of CDKN1A gene in HCT116 p21-/- colorectal cancer cells is identified and shown to be related to the CMS4 subtype of colon cancer. This gene signature is associated with worse relapse-free and overall survival. The findings provide insights into the molecular mechanisms of epithelial-mesenchymal transition and contribute to our understanding of tumor progression.
Article
Oncology
Mattia D'Agostino, David A. Cairns, Juan Jose Lahuerta, Ruth Wester, Uta Bertsch, Anders Waage, Elena Zamagni, Maria-Victoria Mateos, Daniele Dall'Olio, Niels W. C. J. van de Donk, Graham Jackson, Serena Rocchi, Hans Salwender, Joan Blade Creixenti, Bronno van der Holt, Gastone Castellani, Francesca Bonello, Andrea Capra, Elias K. Mai, Jan Durig, Francesca Gay, Sonja Zweegman, Michele Cavo, Martin F. Kaiser, Hartmut Goldschmidt, Jesus Maria Hernandez Rivas, Alessandra Larocca, Gordon Cook, Jesus F. San-Miguel, Mario Boccadoro, Pieter Sonneveld
Summary: In this study, the Revised International Staging system (R-ISS) for intermediate-risk multiple myeloma patients was revised based on the additive value of each single risk feature.
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Immunology
Alicia Landeira-Vinuela, Carlota Arias-Hidalgo, Pablo Juanes-Velasco, Miguel Alcoceba, Almudena Navarro-Bailon, Carlos Eduardo Pedreira, Quentin Lecrevisse, Laura Diaz-Munoz, Jose Manuel Sanchez-Santos, Angela-Patricia Hernandez, Marina L. Garcia-Vaquero, Rafael Gongora, Javier De Las Rivas, Marcos Gonzalez, Alberto Orfao, Manuel Fuentes
Summary: Chronic lymphocytic leukemia (CLL) is a lymphoid neoplasm characterized by the accumulation of mature B cells. The diagnosis is established by the detection of monoclonal B lymphocytes in peripheral blood, even in early stages [monoclonal B-cell lymphocytosis (MBLhi)], and its clinical course is highly heterogeneous. Multiple prognostic factors, such as immunoglobulin heavy chain variable region (IGHV) mutational status, del17p, and TP53 mutations, are related to the observed genetic heterogeneity. In addition, dysregulation of the immune system and the complexity of the tumor microenvironment play critical roles in the onset, progression, and therapy response of CLL.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Manuel Fuentes, Cristina Ruiz-Romero, Sara Misiego, Pablo Juanes-Velasco, Alicia Landeira-Vinuela, Adrian Torres-Roda, Hector Lorenzo-Gil, Maria Gonzalez-Gonzalez, Angela P. Hernandez, Lucia Lourido, Ronald Sjoberg, Elisa Pin, Javier de Las Rivas, Jose Manuel Sanchez-Santos, Peter Nilsson, Francisco J. Blanco
Summary: Rheumatic diseases are common and complex conditions with low sensitivity to clinical diagnosis. This study developed an early diagnosis method for personalized treatment based on the identification of relevant proteins associated with the specific pathologies. By utilizing functional proteomics screening, a panel of 30 serum proteins has been identified as potential biomarkers for rheumatic diseases such as osteoarthritis, rheumatoid arthritis, and psoriatic arthritis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Alicia Landeira-Vinuela, Miguel Alcoceba-Sanchez, Almudena Navarro-Bailon, Carlota Arias-Hidalgo, Pablo Juanes-Velasco, Jose Manuel Sanchez-Santos, Quentin Lecrevisse, Carlos Eduardo Pedreira, Marina L. Garcia-Vaquero, Angela-Patricia Hernandez, Enrique Montalvillo, Rafael Gongora, Javier de las Rivas, Marcos Gonzalez-Diaz, Alberto Orfao, Manuel Fuentes
Summary: Clonal B cell expansion in chronic lymphocytic leukemia may be triggered by persistent antigenic stimulation. Studying the dynamics of the humoral response in these patients can provide information about immunoglobulin levels and identify compromising antigens. This study offers a new perspective for patient stratification and targeted therapy selection.
Article
Medicine, General & Internal
Jaime Lopez-Sanchez, Sonsoles Garrosa-Munoz, Fernando Pardo Aranda, Clara Gene Skrabec, Ricardo Lopez Perez, Patricia Rodriguez-Fortunez, Jose Manuel Sanchez Santos, Luis Munoz-Bellvis
Summary: This study aims to analyze the differences in dose and administration ICG intervals to obtain good-quality NIRFC during LC. The primary outcome is the degree of identification of critical biliary structures during LC. The results of the study will be disseminated to the scientific community through publications, conferences, or other means.
Article
Biochemistry & Molecular Biology
Natalia Alonso-Moreda, Alberto Berral-Gonzalez, Enrique De La Rosa, Oscar Gonzalez-Velasco, Jose Manuel Sanchez-Santos, Javier De Las Rivas
Summary: In the past two decades, there have been many studies on complex biological samples that provide bulk expression signals but fail to identify specific genes in specific cell types due to cellular heterogeneity. To solve this problem, computational techniques have been developed to deconvolve cell mixtures and calculate the relative proportions of cellular components. This study implemented five deconvolution methods and analyzed blood, immune cells, and cancer cells in complex mixture samples. The results show that CIBERSORT is optimized for identifying immune cell types, while LINSEED provides precise gene signatures for immune cell types and cancer cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Hematology
Sandra Muntion, Silvia Preciado, Elena Sanchez-Luis, Luis Corchete, Maria Diez-Campelo, Lika Osugui, Gerardo-Javier Marti-Chillon, Maria-Belen Vidriales, Almudena Navarro-Bailon, Javier De Las Rivas, Fermin Sanchez-Guijo
Summary: This study found that Eltrombopag (EP) not only has direct effects on hematopoietic cells, but also affects the function and properties of mesenchymal stem cells (MSCs), enhancing their ability to support hematopoiesis. These findings are important for the treatment of hematopoietic disorders.
THERAPEUTIC ADVANCES IN HEMATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Marina L. Garcia-Vaquero, Margarida Gama-Carvalho, Francisco R. Pinto, Javier De Las Rivas
Summary: The centrality measures of individual proteins are insufficient to dissect the functional properties of cells, a more comprehensive, relational and context-specific method is needed. The study reveals tissue-specific functional diversification based on the identification of specific protein units.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)